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<h1>
AQUA</h1>

<address>
Jurgen F. Doreleijers, Madison, <a href="mailto:jurgenfd@gmail.com">jurgenfd@gmail.com</a></address>

<address>
Ton Rullmann, Utrecht</address>

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<h2>

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<h2>
Description</h2>
<b>AQUA</b> is a suite of programs for <b>A</b>nalyzing the <b>QUA</b>lity
of biomolecular structures that were determined via NMR spectroscopy. AQUA
was initially developed by Ton Rullmann and Jurgen Doreleijers in the NMR
Spectroscopy Department, Bijvoet Center for Biomolecular Research, Utrecht,
The Netherlands.&nbsp; It is currently maintained and expanded by Jurgen
Doreleijers.
<p>AQUA is capable of calculating the level
of completeness of NOEs of an experimental set of NOEs on the basis of
a three-dimensional structure of the molecule. The easiest way to try the
completeness module of AQUA is via one of the AQUA servers mentioned below.
The service can handle NOE restraints from most NMR software packages (e.g.
X-PLOR, MSI, DYANA and AQUA).
<p>AQUA currently is not able to handle <b>ambiguous NOEs</b> of the type
commonly used by programs such as AMBER, ARIA, CNS, and SANE. Please inform
me if you have a parser for this type of NOEs that can handle the full
set of formats used for ambiguous NOEs.
<p>Output from AQUA can be read and visualized by PROCHECK-NMR, a program
in the PROCHECK suite for assessing the stereochemical quality of protein
structures. The PROCHECK suite was developed in the Biomolecular Structure
and Modelling Group (prof. Thornton), University College, London (<a href="http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html">Procheck
WWW info</a>).
<p>AQUA was developed as part of the Biotech Validation Project. This project
was a collaborative effort of 6 European laboratories, aimed to produce
a coordinated and linked set of software modules that integrate a number
of existing as well as new procedures and protocols for recording, communicating
and validating the models resulting from 3-D structural studies on biomolecules.
The modules should also provide assessment of the intrinsic quality of
the experimental data and the agreement between such data and the derived
atomic models. An important part of the effort was directed at developing
validation criteria by a systematic analysis of published structures. Software
was made available to the community, by distributing source code and data
files.
<p>The Validation Project was funded by the BIOTECH program of DGXII of
the Commission of the European Union, under contract numbers <tt>BIO2CT-920524</tt>
and <tt>BIO4-CT96-018</tt>9.
<p>
<hr>
<h2>
Documentation</h2>

<ul>
<li>
<a href="http://www.biochem.ucl.ac.uk/~roman/procheck_nmr/manual/index.html">Procheck-NMR/AQUA
on-line manual</a> (somewhat dated)</li>

<li>
Please read the following documents to get an idea of whether aqua will
be able to serve your needs before you actually do the install.</li>

<ul>
<li>
<a href="README.html">README</a></li>

<li>
<a href="HOW_TO_INSTALL.html">HOW_TO_INSTALL</a></li>

<li>
<a href="HOW_TO_USE.html">HOW_TO_USE</a></li>

<li>
<a href="NEW.html">NEW</a></li>
</ul>

<li>
The <a href="http://www.bmrb.wisc.edu/~jurgen/Aqua/server">AQUA web
server</a> (described below) has its own documentation.</li>

</ul>

<hr WIDTH="100%">
<h2>
Web server</h2>
The AQUA Validation servers for NMR on the World Wide Web are located in
the Netherlands: <a href="http://www.nmr.chem.uu.nl/users/jurgen/Aqua/server">Bijvoet
Center for Biomolecular Research</a> and here in the USA at the: 
<a href="http://www.bmrb.wisc.edu/~jurgen/Aqua/server">BioMagResBank</a>.
The BMRB installation gets updated first, but let me know if you need to
use an update on one of the others.
<p>
<hr>
<h2>
Source code</h2>
The AQUA suite is currently developed under LINUX (using g++). The complete
package has also been installed and tested on Mac OS X, SGI Irix&nbsp; 6.4 and SunOS
5.7 (both using cc).
<p>An ANSI C&nbsp; compiler is needed for successful compilation (ANSI
style function declarations). The gawk implementation should understand
the -v option and calls to toupper; on some systems you may have to install
gawk, the GNU version of nawk (see documentation from command: <tt>qhelp
gawk</tt>).
<p>Although the code should run on non-Unix systems too, all scripts provided
with the distribution are Unix-only (csh, gawk). Users of e.g. VAX/VMS
will have to set up their own processing scripts. Conversion of restraint
files is done completely via scripts.
<p>If you encounter any problems, but also if you successfully installed
the program, I would like to hear from you. If relevant, please mention
the type of computer and operating system you are using. New AQUA releases
will be mentioned on the <a href="http://mail.bmrb.wisc.edu/bmrblist">BMRB
mailing list</a>. I welcome suggestions about possible additions and improvements
to AQUA so please feel free to mail me.
<p>The latest version of AQUA (3.2) is available <a href="aqua3.2.tar.Z">here</a>.
Some older versions of AQUA are available still available but only on request.
Users are no longer requested to register. NOTE: If you want to use Aqua
in conjunction with Procheck-NMR you have to obtain it (version 3.4 or
higher) separately.
<p>
<hr>
<h2>
External contributions</h2>
The following scripts have been generously contributed and are part of
the AQUA distribution.
<ul>
<li>
Two scripts for splitting (<b>splitpdb</b>) and joining (<b>joinpdb</b>)
MODELs in a PDB file.</li>

<li>
The <b>patchXPLORpdb</b> script for modifying an XPLOR PDB-file to comply
better with the PDB format definition.</li>

<br>The AQUA modules <b>qconvert</b> and <b>aq2x</b> can be used to convert
distance restraint files from/to several formats, including XPLOR, BIOSYM
and DIANA. Currently, support for torsion angle restraints is limited.
The
<b>qconvert</b> module converts torsion angle restraints TO internal
AQUA format. These can be converted to XPLOR using the new aq2xplor-tors
script.</ul>

<hr>
<h3>
Referring to AQUA</h3>
Papers describing AQUA and Procheck-NMR, the quality analysis of 97 NMR
structures with AQUA, and the completeness module of AQUA have been published:
<ul>
<li>
Laskowski R.A., Rullmann J.A.C., MacArthur M.W., Kaptein R. &amp; Thornton
J.M. (1996). "AQUA and PROCHECK-NMR: Programs for checking the quality
of protein structures solved by NMR". <a href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9008363&dopt=Abstract">J.
Biomol. NMR 8, 477-486.</a></li>

<li>
Doreleijers J.F., Rullmann J.A.C. &amp; Kaptein R. (1998). "Quality assessment
of NMR structures: a statistical survey". <a href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=9680482&form=6&db=m&Dopt=b"><i>J.
Mol. Biol.</i> (1998) <b>281</b>:149-164</a>.</li>

<li>
Doreleijers J.F., Raves M.L., Rullmann J.A.C. &amp; Kaptein R. (1999).
"Completeness of NOEs in proteins, a statistical analysis of NMR data".
<i><a href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10610141&dopt=Abstract">J.
Biomol. NMR (1999) 14, 123-132.</a></i></li>
</ul>
Please refer to these publications when using the AQUA software where appropriate.
<p><a name="Sponsors"><b>Sponsors</b></a></p>

<a href="http://sourceforge.net">
<img src="http://sflogo.sourceforge.net/sflogo.php?group_id=198807&amp;type=1" width="88" height="31" border="0" alt="SourceForge.net Logo"></a><hr>
<p>Contact the <a href="mailto:jurgenfd@gmail.com">author</a>
for help, when required.
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